Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 157

10 diseases · 28 shared-gene connections
10 Diseases
13 Unique genes
0.341 Avg. similarity score
Familial infantile myofibromatosis Most-connected disease (9 links)
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Disease Searched: Myeloid neoplasm associated with pdgfrb rearrangement Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Familial infantile myofibromatosis 9 9 1
Kosaki overgrowth syndrome 8 8 1
Premature aging syndrome, penttinen type 8 8 1
Myeloid neoplasm associated with pdgfrb rearrangement 6 6 2
Myofibromatosis, infantile 1 6 6 1
Myeloproliferative disorder chronic with eosinophilia 5 5 2
Acroosteolysis 4 4 2
Calcifications in basal ganglia 4 4 3
Hypereosinophilic syndrome 3 3 7
Primary melanoma of the central nervous system 3 3 4

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
PDGFRB 10 / 10 Acroosteolysis, Calcifications in basal ganglia, Familial infantile myofibromatosis, Hypereosinophilic syndrome and 6 more
ETV6 3 / 10 Hypereosinophilic syndrome, Myeloid neoplasm associated with pdgfrb rearrangement, Myeloproliferative disorder chronic with eosinophilia
What do these columns mean?
Connections in cluster
How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners
How many of those links are statistically significant (FDR q < 0.05).
Curated genes
Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes)
How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y)
x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count
Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment
Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value
Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster)
Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster)
Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Pathways in cancer
NOTCH2, PDGFRB, PDGFRA, FGFR1, JAK1, GNAQ, ESR1
 KEGG 7 / 533 12.1× 4.43e-7 2.06e-5 ✓ sig.
Constitutive Signaling by Aberrant PI3K in Cancer
PDGFRB, PDGFRA, FGFR1, ESR1
 Reactome 4 / 75 49.3× 9.61e-7 4.03e-5 ✓ sig.
PIP3 activates AKT signaling
PDGFRB, PDGFRA, FGFR1, ESR1
 Reactome 4 / 93 39.7× 2.28e-6 8.44e-5 ✓ sig.
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
PDGFRB, PDGFRA, FGFR1, ESR1
 Reactome 4 / 103 35.9× 3.44e-6 1.20e-4 ✓ sig.
RAF/MAP kinase cascade
PDGFRB, PDGFRA, FGFR1, JAK1
 Reactome 4 / 124 29.8× 7.20e-6 2.23e-4 ✓ sig.
Central carbon metabolism in cancer
PDGFRB, PDGFRA, FGFR1
 KEGG 3 / 71 39.0× 5.43e-5 1.16e-3 ✓ sig.
Rap1 signaling pathway
PDGFRB, PDGFRA, FGFR1, GNAQ
 KEGG 4 / 211 17.5× 5.85e-5 1.23e-3 ✓ sig.
Melanoma
PDGFRB, PDGFRA, FGFR1
 KEGG 3 / 73 38.0× 5.90e-5 1.24e-3 ✓ sig.
EGFR tyrosine kinase inhibitor resistance
PDGFRB, PDGFRA, JAK1
 KEGG 3 / 80 34.6× 7.76e-5 1.55e-3 ✓ sig.
Gap junction
PDGFRB, PDGFRA, GNAQ
 KEGG 3 / 89 31.1× 1.07e-4 1.99e-3 ✓ sig.
Calcium signaling pathway
PDGFRB, PDGFRA, FGFR1, GNAQ
 KEGG 4 / 254 14.5× 1.20e-4 2.19e-3 ✓ sig.
Prostate cancer
PDGFRB, PDGFRA, FGFR1
 KEGG 3 / 98 28.3× 1.42e-4 2.50e-3 ✓ sig.
Downstream signal transduction
PDGFRB, PDGFRA
 Reactome 2 / 29 63.7× 4.32e-4 5.96e-3 ✓ sig.
PI3K-Akt signaling pathway
PDGFRB, PDGFRA, FGFR1, JAK1
 KEGG 4 / 361 10.2× 4.63e-4 6.30e-3 ✓ sig.
Breast cancer
NOTCH2, FGFR1, ESR1
 KEGG 3 / 148 18.7× 4.79e-4 6.46e-3 ✓ sig.

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
positive regulation of chemotaxis
PDGFRB, PDGFRA, TREM2
 GO:0050921 3 / 21 205× 3.47e-7 3.59e-5 ✓ sig.
positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway
PDGFRB, PDGFRA
 GO:0038091 2 / 3 958× 1.34e-6 1.09e-4 ✓ sig.
metanephric glomerular capillary formation
PDGFRB, PDGFRA
 GO:0072277 2 / 3 958× 1.34e-6 1.09e-4 ✓ sig.
positive regulation of calcium-mediated signaling
PDGFRB, PDGFRA, TREM2
 GO:0050850 3 / 38 113× 2.19e-6 1.63e-4 ✓ sig.
peptidyl-tyrosine phosphorylation
PDGFRB, PDGFRA, FGFR1
 GO:0018108 3 / 39 111× 2.37e-6 1.74e-4 ✓ sig.
positive regulation of ERK1 and ERK2 cascade
NOTCH2, PDGFRB, PDGFRA, TREM2
 GO:0070374 4 / 201 28.6× 8.61e-6 4.85e-4 ✓ sig.
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
PDGFRB, PDGFRA, FGFR1, TREM2
 GO:0051897 4 / 217 26.5× 1.16e-5 6.12e-4 ✓ sig.
cardiac myofibril assembly
PDGFRB, PDGFRA
 GO:0055003 2 / 13 221× 3.47e-5 1.40e-3 ✓ sig.
retina vasculature development in camera-type eye
PDGFRB, PDGFRA
 GO:0061298 2 / 15 192× 4.67e-5 1.76e-3 ✓ sig.
protein autophosphorylation
PDGFRB, PDGFRA, FGFR1
 GO:0046777 3 / 113 38.2× 5.89e-5 2.09e-3 ✓ sig.
positive regulation of MAP kinase activity
PDGFRB, FGFR1
 GO:0043406 2 / 25 115× 1.33e-4 3.79e-3 ✓ sig.
positive regulation of osteoclast differentiation
NOTCH2, TREM2
 GO:0045672 2 / 28 103× 1.67e-4 4.46e-3 ✓ sig.
platelet-derived growth factor receptor signaling pathway
PDGFRB, PDGFRA
 GO:0048008 2 / 33 87.1× 2.33e-4 5.65e-3 ✓ sig.
positive regulation of cell population proliferation
NOTCH2, PDGFRB, PDGFRA, FGFR1
 GO:0008284 4 / 532 10.8× 3.78e-4 7.87e-3 ✓ sig.
skeletal system morphogenesis
PDGFRA, FGFR1
 GO:0048705 2 / 45 63.9× 4.35e-4 8.64e-3 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Myeloid neoplasm associated with pdgfrb rearrangement Myeloproliferative disorder chronic with eosinophilia 0.667 2 8.34e-9 6.60e-8 ✓ sig.
Hypereosinophilic syndrome Myeloid neoplasm associated with pdgfrb rearrangement 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Hypereosinophilic syndrome Myeloproliferative disorder chronic with eosinophilia 0.250 2 1.75e-7 1.18e-6 ✓ sig.
Myofibromatosis, infantile 1 Premature aging syndrome, penttinen type 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial infantile myofibromatosis Premature aging syndrome, penttinen type 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial infantile myofibromatosis Kosaki overgrowth syndrome 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Familial infantile myofibromatosis Myofibromatosis, infantile 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Kosaki overgrowth syndrome Myofibromatosis, infantile 1 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Kosaki overgrowth syndrome Premature aging syndrome, penttinen type 0.500 1 6.46e-5 1.98e-4 ✓ sig.
Acroosteolysis Premature aging syndrome, penttinen type 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Myeloid neoplasm associated with pdgfrb rearrangement Myofibromatosis, infantile 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Kosaki overgrowth syndrome Myeloproliferative disorder chronic with eosinophilia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Myeloproliferative disorder chronic with eosinophilia Premature aging syndrome, penttinen type 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial infantile myofibromatosis Myeloproliferative disorder chronic with eosinophilia 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Myeloid neoplasm associated with pdgfrb rearrangement Premature aging syndrome, penttinen type 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Kosaki overgrowth syndrome Myeloid neoplasm associated with pdgfrb rearrangement 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acroosteolysis Familial infantile myofibromatosis 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Familial infantile myofibromatosis Myeloid neoplasm associated with pdgfrb rearrangement 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acroosteolysis Myofibromatosis, infantile 1 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Acroosteolysis Kosaki overgrowth syndrome 0.333 1 1.29e-4 3.27e-4 ✓ sig.
Calcifications in basal ganglia Myofibromatosis, infantile 1 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Calcifications in basal ganglia Kosaki overgrowth syndrome 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Calcifications in basal ganglia Premature aging syndrome, penttinen type 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Calcifications in basal ganglia Familial infantile myofibromatosis 0.250 1 1.94e-4 4.41e-4 ✓ sig.
Kosaki overgrowth syndrome Primary melanoma of the central nervous system 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Premature aging syndrome, penttinen type Primary melanoma of the central nervous system 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Familial infantile myofibromatosis Primary melanoma of the central nervous system 0.200 1 2.58e-4 5.38e-4 ✓ sig.
Familial infantile myofibromatosis Hypereosinophilic syndrome 0.125 1 4.52e-4 8.26e-4 ✓ sig.